This is expected behaviour.
If you are using the same equipment between the two sequences, simply set multiple targets within the one sequence, making sure you check the slew and centre options for the second target (and third, and fourth, and fifth etc). This is what SGP is designed to do - multiple targets within a sequence.
The new planning tools are terrific at helping set start/stop times or altitudes.
You can also import targets from one sequence into another.
I haven’t checked the manual for some time and not sure if the new planning tools are yet described. However much of your question relates to long-established principles and is well detailed in the manual. On screen tool tips are very helpful. There is also a growing corpus of helpful web tutorials.
Apologies if I’ve not understood your question.